[gmx-users] "Fatal error: Atomtype CH2 not found" in grompp command

Elissa Fink elissa.fink.14 at cnu.edu
Tue Aug 16 21:04:29 CEST 2016

Dear Gromacs users,

I am simulating a protein-ligand complex and I am performing the grompp
command before adding ions to the system:
>gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

and I get the error:

"Source code file:/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,

Fatal error:
Atomtype CH2 not found"

I checked for CH2 groups in the solv.gro file and there are 4 in tryptophan
residues. I am running the complex with the amber99sb-ildn force field. I
checked the force field .rtp file for the tryptophan name of a CH2 group.
It has CA, so I changed the 4 CH2 groups to CA in the solve.gro file. I
reran the grompp command above and got the same error. This makes me think
the problem is not the tryptophan CH2's in the solve.gro file.

Any recommendations for addressing the CH2 atom type not found?

Thanks in advance,
Elissa Fink

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